Police officers who responded to the shooting on Saturday afternoon found the body of the suspected gunman in an area near the restaurant, Twin Falls city public information officer Josh Palmer said.
He did not know if the suspect was included in the fatality count.
Officials were still working on notifying the family members of victims and so were not yet releasing the names, ages or other details about the people hurt in the shooting, Palmer said.
Twin Falls Police Chief Matthew Hicks said in a news conference on Saturday. Police were still trying to determine the shooter's identity and motive.
"It was a very chaotic scene."
The shooting was reported on Saturday afternoon near a busy shopping area in Twin Falls.
Earlier in the day police issued a waring, urging people to avoid the area.
"Our department is responding to an active shooter incident in the area of In-N-Out, an alert on Facebook said.
"We are asking all residents and visitors to avoid the area so officers and first responders can work safely."
Lane Koehn, 34, said he was at a stoplight near the In-N-Out when he saw a person with an AR-style rifle emerge from the drive-thru. A man with a pistol started firing at the shooter.
He then saw someone in an In-N-Out uniform drag a person, also uniformed, bleeding from a gunshot wound in her chest across the car park.
"She was pretty bad off, but I don't know. I hope she made it," Koehn said.
Koehn said he was told by police to evacuate because the shooter was still active.
The shooter fired at least three or four rounds, he said.
Video taken by a driver from across the street captured a shooter, dressed in black, walking up to a white car carrying a long rifle, opening the driver-side door and popping the trunk.
The person then walked to the boot and reached inside. At that point the driver who shot the video left quickly, fearing that the man might be getting more weapons.
Twin Falls resident Haley Dodaro, 43, and her mother went to In-N-Out for lunch on Saturday and while waiting in the drive-thru line, saw people running across the road and workers bolting out of the restaurant. At first Dodaro thought there might have been a fire, but then a man directing traffic in a reflective vest said there was a shooter.
"People were running out crying and screaming. It was very scary," Dodaro said in a text message to The Associated Press.
Nayeli Rodriguez, 40, of Burley, was inside waiting for food with her daughters when she heard shots from the kitchen. An employee said it was a shooting and told people to get down.
Rodriguez said an older man tried to protect her and her daughters, and they were among the last to run outside.
"We were trying to get as far as we could and some angels let us in their car," Rodriguez said, also via text message.
The In-N-Out opened just about a week earlier, on July 24, as part of the company's recent expansion to Idaho.
Twin Falls, a city of about 56,000 people, is about 200km southeast of Boise.
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